Course content
The course will provide an entry-level introduction to a wide range of analytical techniques for massively parallel sequencing, including basic Linux commands. We will pair lectures on the theory of analysis algorithms with practical computational exercises demonstrating the use of common tools for analyzing data from each of several common sequencing study designs.

Topics covered will include:

Basic Linux usage
NGS read-to-reference alignment (genomic and RNA-Seq)
Variant calling in populations
De novo assembly of RNA-sequence data
Reference-guided RNA-Seq expression analysis
Data management
Analysis techniques covered will focus mostly on data from the Illumina platform, but we will discuss other sequencing platforms and the advantages and challenges to using their data.